|
| Status |
Public on Oct 01, 2019 |
| Title |
PfOO-3 |
| Sample type |
SRA |
| |
|
| Source name |
Oocyst Sporozoites
|
| Organism |
Plasmodium falciparum 3D7 |
| Characteristics |
tissue: Oocyst Sporozoites
|
| Treatment protocol |
Sporozoites were purified twice with sequential Accudenz discontinuous density gradients.
|
| Growth protocol |
Plasmodium yoelii or Plasmodium falciparum gametocytes were fed to Anopheles stephensi mosquitoes, and infections were allowed to proceed for 10 days (oocyst sporozoites) or 14 days (salivary gland sporozoites)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were lysed and RNA purified using a Qiagen Rneasy Kit with additional DNaseI on-column digestions.
A barcoded library was made from each sample by using the Illumina TruSeq Stranded mRNA Library Prep Kit (Illumina, Cat# RS-122-2101) according to the manufacturer's protocol. qPCR was performed to determine the concentration of each library and an equimolar pool was made of all libraries. The library pool was sequenced on an Illumina HiSeq 2500 in Rapid Run mode according to the manufacturer's protocol.
100 nt single read RNA-sequencing
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
PfOO-3
|
| Data processing |
Tophat2: each batch of reads was aligned to the reference genome (PY17X v32 or PF3D7 v30)
htseq-count:These reads were then aligned to the annotated transcriptome of P. yoelii (v32 from PlasmoDB) or P. falcipari, (v30 from PlasmoDB) using htseq-count. We utilized the Union method for reads overlapping annotated transcripts.
DESeq2: The count files from htseq-count were merged and compared across conditions using DESeq2. Samples were grouped and compared between Oocyst sporozoites and salivary gland sporozoites within the same organism. These were compared by the parametric fit type with outlier replacement turned on to normalize variance between the count files.
Genome_build: All data sets were aligned to the PY17X Genome v32 or PF3D7 Genome v30 obtained from PlasmoDB. The same version of the annotated transcriptome was used for the ht-seq count step of the analysis.
Supplementary_files_format_and_content: The processed data file contains the output from the DESeq2 program. These have been combined with the normalized read outputs for each run, as well as supplemented with the means and standard error of the mean for each batch.
|
| |
|
| Submission date |
Apr 24, 2018 |
| Last update date |
Nov 14, 2019 |
| Contact name |
Scott E. Lindner |
| E-mail(s) |
Scott.Lindner@psu.edu
|
| Phone |
8148674062
|
| Organization name |
Penn State University
|
| Department |
Biochemistry and Molecular Biology
|
| Street address |
W224 Millennium Science Complex
|
| City |
University Park |
| State/province |
Pennsylvania |
| ZIP/Postal code |
16802 |
| Country |
USA |
| |
|
| Platform ID |
GPL24926 |
| Series (1) |
| GSE113582 |
Extensive Transcriptional and Translational Regulation Occur During the Maturation of Malaria Parasite Sporozoites |
|
| Relations |
| BioSample |
SAMN08975578 |
| SRA |
SRX3990051 |
